Method for diagnosing acute lymphomic leukemia (all) using mir-222

ABSTRACT

Disclosed are compositions and methods for reducing the proliferation of ALL cancer cells through targeted interactions with ALL1 fusion proteins.

CROSS-REFERENCE TO RELATED APPLICATIONS

This is a divisional application of U.S. Ser. No. 12/664,531 having a 37CFR §1.371 filing date of Jan. 8, 2010, now U.S. Pat. No. ______ issued______, ______, 2011, which was a national stage application filed under37 CFR §1.371 of international application PCT/US2008/066870 filed Jun.13, 2008, which claims the priority to U.S. Provisional Application Ser.No. 60/934,707 filed Jun. 15, 2007, the entire disclosures of which areexpressly incorporated herein by reference.

GOVERNMENT SUPPORT

The invention made with government support under Grant No. RO1 CA128609,awarded by the National Cancer Institute. The Government has certainrights in the invention.

FIELD OF THE INVENTION

The present invention provides compositions and methods for modulationof small non-coding RNAs, particularly pri-miRNAs. In particular, thisinvention relates to compounds, particularly oligomeric compounds,which, in some embodiments, hybridize with or sterically interfere withnucleic acid molecules comprising or encoding small non-coding RNAtargets, including pri-miRNAs.

SEQUENCE LISTING

The patent application contains a “Sequence Listing” section. A copy ofthe “Sequence Listing” is available in electronic form from the USPTOweb site (seqdata.uspto.gov/sequence). A paper copy of the sequencelisting and a computer-readable form of the sequence listing are hereinincorporated by reference. An electronic copy of the “Sequence Listing”will also be available from the USPTO upon request and payment of thefee set forth in 37 CFR 1.19(b)(3). The ASCII copy, created on Jul. 23,2008, is named 604_(—)29185_SEQ_LIST_(—)11011.txt, and is 8 KB in size.

BACKGROUND OF THE INVENTION

Acute leukemia is a rapidly progressive malignant disease of the bonemarrow and blood that results in the accumulation of immature,functionless cells, called blast cells, in the marrow and blood. Theaccumulation of blast cells in the marrow blocks normal blood celldevelopment. As a result, red cells, white cells and platelets are notproduced in sufficient numbers. When the disease originates in a marrowlymphocyte progenitor cell, it results in acute lymphoblastic leukemia(ALL) and when the disease originates in a myeloid progenitor, itresults in acute myelogenous leukemia (AML).

ALL is a rapidly progressive cancer that starts by the malignanttransformation of a marrow lymphocyte. ALL is the most common type ofchildhood leukemia, with 3,000 new cases per year in all age groups. Thetransformed, now malignant, cell multiplies and accumulates in themarrow as leukemic lymphoblasts. The lymphoblasts block normal bloodcell-formation in the marrow, resulting in insufficient production ofred cells, white cells and platelets.

High-grade lymphomas, also known as aggressive lymphoma, include severalsubtypes of lymphoma that progress relatively rapidly if untreated.These subtypes include, e.g., AIDS-associated lymphoma, anaplastic largecell lymphoma, Burkitt's lymphoma, diffuse large cell lymphoma,immunoblastic lymphoma, lymphoblastic lymphoma and small noncleaved celllymphomas. Compared to diffuse large B-cell lymphomas, high-gradelymphomas behave more aggressively, require more intensive chemotherapy,and occur more often in children. Because rapidly dividing cells aremore sensitive to anti-cancer agents and because the young patientsusually lack other health problems, some of these lymphomas show adramatic response to therapy. Acute lymphoblastic leukemia andhigh-grade lymphoma are the most common leukemias and lymphomas inchildren. These diseases are, for the most part, polyclonal, suggestingthat only a few genetic changes are sufficient to induce malignancy.

ALL-1, also termed MLL has been cloned from chromosome band 11q23,recurrent site involved in multiple chromosome abnormalities associatedwith both acute lymphoblastic (ALL) and acute myeloblastic (AML)leukemia (1, 2). The chromosome translocation results in the fusion ofthe ALL1 gene with one of more than 50 different partner genes and theproduction of leukemogenic proteins composed of the N-terminal All1sequence and a portion of the partner protein encoded by the segment ofthe gene positioned 3′ to the breakpoint (ibid). The most prevalent ALL1rearrangement in ALL is the ALL1/AF4 chimeric gene resulting from thet(4;11) chromosome translocation. This rearrangement is associated withvery poor prognosis in infants and adults (3). The molecular pathwaysderegulated by the All1 fusion protein, which bring about theaggressiveness of the disease are still largely unknown.

miRNAs are short 20-22 nucleotide RNA that negatively regulate the geneexpression at the post-transcriptional level by base pairing to the 3′untranslated region of target messenger RNAs. More than 400 miRNAs havebeen identified in human and they are evolutionarily conserved. It hasbeen shown that miRNAs regulate various physiological and pathologicalpathways such as cell differentiation, cell proliferation andtumorigenesis (reviewed in 4). Extensive studies to determine expressionprofile of miRNAs in human cancer has revealed cell-type specific miRNAfingerprint found in B cell chronic lymphocytic leukemia (B-CLL), breastcancer, colon cancer, gastric cancer, glioblastoma, hepatocellularcarcinoma, papillary thyroid cancer, and endocrine pancreatic tumors(reviewed in 5).

Calin et al. showed that although miRNA genes represent only 1% of themammalian genome, more than 50% of miRNA genes are located within regionassociated with amplification, deletion and translocation in cancer (6).Such somatic changes of miRNA genes definitively attribute to thespecific expression pattern found in cancer. Additional factors, whichattribute to the cancer specific deregulation of miRNAs, are unknown,although the most obvious candidate is transcriptional control. Otherpossibility is that miRNA maturation is such factor. Micro RNAbiogenesis begins with a primary transcript, termed pri-miRNA, which isgenerated by RNA polymerase II (review in 7). Within the pri-miRNA, themiRNA itself is contained within a ˜60-80 nucleotide that can fold backon itself to form a stem-loop hairpin structure. This hairpin structureis recognized and excised from pri-miRNA by the microprocessor complexcomposed of nuclear RNase III enzyme, Drosha and its binding partnerDGCR8. The excised miRNA hairpin, referred to as pre-miRNA, istransported to the cytoplasm in association with RAN-GTP and Exportin 5,where it is further processed by a second RNase III enzyme, Dicer, whichreleases a 22 nucleotide mature duplex RNA with 5′ phosphate and2-nucleotide 3′ overhang. The antisense RNA strand is incorporated intothe RISC complex, which target it to mRNA(s) by base-pairing andconsequently interfere with translation of the mRNA or cleave it. Inprinciple, any step during this maturation process could affect miRNAproduction.

Consequently, there is a need for agents that regulate gene expressionvia the mechanisms mediated by small non-coding RNAs. Identification ofoligomeric compounds that can increase or decrease gene expression oractivity by modulating the levels of miRNA in a cell is thereforedesirable.

The present invention therefore provides oligomeric compounds andmethods useful for modulating the levels, expression, or processing ofpri-miRNAs, including those relying on mechanisms of action such as RNAinterference and dsRNA enzymes, as well as antisense and non-antisensemechanisms. One having skill in the art, once armed with this disclosurewill be able, without undue experimentation, to identify compounds,compositions and methods for these uses.

SUMMARY OF THE INVENTION

The present invention is based on the discovery that All1 fusionprotein-mediates the recruitment of the enzyme Drosha to target genesencoding specific miRNAs. This recruitment is now believed to be thecause for the enhanced expression of the relevant miRNAs.

In one aspect, there is provided agents that regulate gene expressionvia the mechanisms mediated by small non-coding RNAs. Identification ofoligomeric compounds that can increase or decrease gene expression oractivity by modulating the levels of miRNA in a cell is thereforedesirable.

In a particular aspect, there is provided oligomeric compounds andmethods useful for modulating the levels, expression, or processing ofpri-miRNAs, including those relying on mechanisms of action such as RNAinterference and dsRNA enzymes, as well as antisense and non-antisensemechanisms. One having skill in the art, once armed with this disclosurewill be able, without undue experimentation, to identify compounds,compositions and methods for these uses.

In a particular aspect, there is provided oligomeric compounds,especially nucleic acid and nucleic acid-like oligomeric compounds,which are targeted to, or mimic, nucleic acids comprising or encodingsmall non-coding RNAs, and which act to modulate the levels of smallnon-coding RNAs, particularly pri-miRNAs, or interfere with theirfunction.

In a particular aspect, there is provided oligomeric compounds,especially nucleic acid and nucleic acid-like oligomeric compounds,which are targeted to pri-miRNAs, and which act to modulate the levelsof pri-miRNAs, or interfere with their processing or function.

In a particular aspect, there is provided oligomeric compounds thattarget a region flanking or overlapping a Drosha recognition regionwithin a pri-miRNA.

Additionally, there is provided oligomeric compounds that target aregion flanking or overlapping a Drosha cleavage site. There is alsoprovided oligomeric compounds that increase levels of a pri-miRNA. Forexample, the present invention provides oligomeric compounds 15 to 30nucleobases in length targeted to a Drosha recognition region within apolycistronic pri-miRNA transcript. The polycistronic pri-miRNAtranscript can be that from which the miRNAs listed in Table 1 arederived.

In particular embodiments, the Drosha recognition region can be one ormore of the miRNAs listed in Table 1. Such oligomeric compounds may beantisense oligonucleotides, and may contain one or more chemicalmodifications. Additionally, such oligomeric compounds are capable ofincreasing pri-miRNA levels.

Also provided are methods of modulating the levels of small non-codingRNAs, particularly pri-miRNAs, in cells, tissues or animals comprisingcontacting the cells, tissues or animals with one or more of thecompounds or compositions of the invention.

Further provided are methods of modulating the levels of miRs derivedfrom a polycistronic pri-miR transcript in a cell comprising selecting apolycistronic pri-miR transcript, selecting a Drosha recognition regionof a single miRNA derived from the selected polycistronic pri-miRtranscript, selecting an oligomeric compound 15 to 30 nucleotides inlength targeted to or sufficiently complementary to the selected Drosharecognition region, and contacting the cell with the oligomericcompound.

Such methods include modulating the levels of a single mature miRNAderived from the selected polycistronic pri-miRNA, or alternativelymodulating the levels of two or more mature miRNAs derived from theselected polycistronic pri-miRNA.

Also provided are methods of modulating the levels of pri-miRNAs fromthose listed in Table 1 comprising contacting a cell with an oligomericcompound targeted to or sufficiently complementary to Drosha-recognitionregions on such pri-miRNAs.

There is also provided herein methods for selectively modulating asingle member of a miR family in a cell comprising selecting a member ofa miR family derived from a pri-miR transcript, identifying one or moreoligomeric compounds targeted to or sufficiently complementary to theDrosha recognition region of a the selected pri-miR transcript, whereinthe identified oligomeric compounds lack sufficient complementarity tothe Drosha recognition regions of pri-miR transcripts from which othermembers of the miR family are derived, and contacting the cell with suchan identified oligomeric compound.

There is also provided herein oligomeric compounds comprising a firststrand and a second strand wherein at least one strand contains amodification and wherein a portion of one of the oligomeric compoundstrands is capable of hybridizing to a small non-coding RNA targetnucleic acid.

There is also provided herein oligomeric compounds comprising a firstregion and a second region and optionally a third region wherein atleast one region contains a modification and wherein a portion of theoligomeric compound is capable of hybridizing to a small non-coding RNAtarget nucleic acid.

There is also provided herein methods for identifying oligomericcompounds capable of modulating pri-miRNA levels. A pri-miRNA isselected, and oligomeric compounds are designed such that they aretargeted to or sufficiently complementary to various target segmentswithin a pri-miRNA sequence, including oligomeric compounds targeted toand overlapping the mature miRNA sequence within the pri-miRNA. Anincrease in the level of a pri-miRNA in cells contacted with theoligomeric compounds as compared to cells not contacted with theoligomeric compounds indicates that the oligomeric compound modulatesthe pri-miRNA level.

There is also provided herein methods for identifying small moleculescapable of modulating pri-miRNA levels. A pri-miRNA is selected, andsmall molecules are evaluated for their ability of modulate pri-miRNAlevels. The small molecules may bind to the regions of the pri-miRcontaining or overlapping the mature miRNA sequence, or the Drosharecognition region. An increase in the level of a pri-miRNA in cellscontacted with the small molecules as compared to cells not contactedwith the small molecules indicates that the small molecule modulates thepri-miRNA levels.

There is also provided herein a decoy for treating and/or preventing ALLand -related diseases.

These as well as other important aspects of the invention will becomemore apparent from the following detailed description.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawings will be provided by the Office upon request and paymentof the necessary.

FIG. 1. RNase protection assay for the detection of miR-191 and miR-155in leukemic cell lines with ALL-1 rearrangements.

20 μg of total RNAs were hybridized overnight at 43° C. with in vitrotranscribed anti-sense probe of miR-191 or miR-155 and subsequentlytreated with RNase. Protected probe fragments were resolved on a 15%polyacrylamide gel containing 8M urea. End-labeled φX174/Hinf I was usedas a molecular weight marker. Because of the compression of the markerfor sizes larger than 200 nucleotides, only fragments of 151 nt andbelow are shown. As a loading control, 10 μg of total RNA was alsosubjected to hybridization with Cyclophillin probe.

FIGS. 2A and 2B. Purification of Drosha protein from ALL-1-rearrangedleukemic cells by Immunoprecipitation with anti-Drosha Ab.

FIG. 2A) Western blot detection of immunoprecipitated proteins. Ab 169reacting with All1 N terminal epitope was utilized for the detection ofAll1/Af4 and of All1/Af9. For unambiguous identification of Drosha,recombinant Drosha exogenously expressed in K562 cells transfected withpCK-Drosha-Flag plasmid was purified by IP (Drosha:FLAG). 20 μg nuclearextracts of leukemic cells or around 2.5 μg of immuno-purified Droshawere used in the analysis. Note that endogenous Drosha was purified fromnuclear extracts while Drosha:FLAG was from whole cell lyzate.

FIG. 2B) Western blot detection of proteins immunoprecipitated withanti-Drosha Ab from SEMK2 nuclear extracts treated either with RNase orDNase.

FIG. 3. In vitro cleavage assays of Drosha immuno-purified fromplasmid-transfected cells and from ALL1-associated leukemic cell lines.

Equal amounts of Drosha, determined by Western analysis (FIG. 2A) wereused in all reactions; the corresponding volumes of the non-dilutedsamples were 10 μl of Drosha:FLAG, 5 μl of SEMK2 Drosha and 20 μl ofPER377 Drosha. Cleaved products of miR-191 and miR-155 were resolved ondenaturing 9% polyacrylamide gel (FIG. 3, left). The cleaved productswere excised from the gel, electro-eluted, and subjected to furthercleavage with recombinant Dicer enzyme. 15% denaturing gel was used toresolve and identify the 22 nucleotides mature products (FIG. 3, right).

FIGS. 4A-E. All1/Af4-dependent localization of Drosha in miR-191 andmiR-23a genomic loci and the effect of All1/Af4 knockdown on Drosharecruitment.

FIG. 4 a) Elimination of most of the All1/Af4 protein from SEMK2 cellstreated with SEMJ siRNA.

FIGS. 4B-4D) ChIP analysis for determination of recruitment of normalAll1, All1/Af4 and drosha proteins to genomic loci encoding miR-191,miR-155, miR-23a and miR-27a. Chromatins tested were from SEMK2 cellstreated with the non-functional siRNA MVJ, or from cells treated withthe SEMJ siRNA which knocks down most of All1/Af4.

FIG. 4E) The sequence listings for Nucleotide Sequence of Human Genomicfragment encoding microRNA-191 [SEQ ID NO.: 17], which was cloned intopGEM3Z vector (Promega) and was used as a probe in RNase protectionassay; Nucleotide Sequence of Human Genomic fragment encodingmicroRNA-155 [SEQ ID NO.: 18], which was cloned into pGEM3Z vector(Promega) and was used as a probe in RNase protection assay; NucleotideSequence of Human Genomic fragment encoding microRNA-23a [SEQ ID NO.:19], which was cloned into pGEM3Z vector (Promega) and was used as aprobe in RNase protection assay; Nucleotide Sequence of Human Genomicfragment encoding microRNA-27a [SEQ ID NO.: 20], which was cloned intopGEM3Z vector (Promega) and was used as a probe in RNase protectionassay.

FIG. 5. Effect of All1/Af4 knockdown on accumulation of pri miR-191.

Abundance of the precursors pri miR-191, pri miR-155, pri miR-23a andpri miR-27a, as well as of their processed products, was tested in SEMK2cells treated with the non-active MVJ siRNA, or knocked down for eitherAll1/Af4 (SEMJ) or Drosha. The RNAs were identified by RNase protectionassay (see text). Note that Drosha knockdown increased the abundance ofall primary transcripts. In contrast, knockdown of All1/Af4 (SEMJ) wasassociated with higher abundance of pri miR-191 and pri miR-23a.

FIG. 6. Upregulation of miR-191 in leukemic cell lines with the t(4;11)chromosome translocation.

Northern analysis of RNAs (aliquots of 20 μg) from MV4;11, RS4;11, andSEMK2-all pro-B cells with t(4;11), from the pro-B cells REH and 380,and from the pre-B cell line 697. RNAs were separated on 20% denaturingpolyacryl amide gel and electro-blotted into a Nylon membrane. The 22nucleotides miR-191 was identified by hybridization to an end-labelledoligonucleotide. Similar Northern analysis for KG1 and K562 cells, bothlacking ALL1 rearrangement, indicated low level of expression like thatof 380 and 697 cells (not shown).

FIGS. 7A and 7B. Identification by RNase protection assay (RPA) of miRprecursor and processed RNAs produced in vivo (left gels), or producedby in vitro cleavage with Drosha and Dicer (right gels).

Sequences of miR-191 [SEQ ID NO: 21] probe (FIG. 7A) and miR-155 probe[SEQ ID NO: 22] (FIG. 7B), synthesized by in vitro transcription with T7RNA polymerase are shown. The mature micro RNA and the flanking pGEM 3Zvector sequences are shown in red and grey letters, respectively.Restriction sites used to generate run-off transcripts are indicated.Vertical arrows indicate Drosha cleavage sites, predicted from ref. 11for miR-191 or reported in ref. 9 for miR-155. Predicted RNase protectedfragments of the products of hybridization between cell RNA anduniformly labeled probes, and of in vitro cleavage products (by Droshaor Dicer) are summarized below the probe sequence. Products of the RPAand of the in vitro cleavage assays were resolved on a single denaturinggel. For the in vitro cleavage assay, Drosha:FLAG was used. The cleavageproducts of 64 and 61 nt, derived from miR-191 and miR-155 probes,respectively, were digested with recombinant Dicer after excision andpurification from the gel. In the assay for miR-155, the RPA protectedfragments of 53 and 61 nt and the in vitro cleavage products could notbe resolved in the gel and their relative positions are marked witharrows.

FIGS. 8A and 8B. miR-23a probe [SEQ ID NO: 23] (FIG. 8A) and miR-27aprobe [SEQ ID NO: 24] (FIG. 8B) used in RNase Protection Assay in FIG.5.

The mature micro RNA and the flanking pGEM 3Z vector sequences are shownin red and grey letters, respectively. The pGEM 3Z recombinantsharboring miR-23a hairpin and miR-27a hairpin were linearlized with NaeIand Bsu36I, respectively and were used as the templates to generateanti-sense probes with SP6 RNA polymerase.

DETAILED DESCRIPTION OF THE INVENTION

A description of particular embodiments of the invention follows.

As used herein, the term “Drosha recognition region” within a pri-miRNAtranscript encompasses the mature miRNA as well as up to 25 nucleotidesin the 5′ direction relative to the 5′ Drosha cleavage site of suchmature miRNA, and up to 50 nucleotides in the 3′ direction relative tothe 3′ Drosha cleavage site of such mature miRNA. In additionalembodiments, the Drosha recognition region encompasses the mature miRNAand up to 15 nucleotides in the 5′ direction relative to the 5′ Droshacleavage site of such mature miRNA, and up to 40 nucleotides in the 3′direction relative to the 3′ Drosha cleavage site of such mature miRNA.In some aspects, the Drosha recognition region is a region stronglyaffected by oligomeric compounds targeted to this region, i.e. thetargeting of oligomeric compounds to this region of a pri-miRNA resultsin a greater than 3.5-fold increase in the level of the pri-miRNA. Inother aspects, the level of the pri-miRNA is moderately affected byoligomeric compounds targeted to this region, i.e. the targeting ofoligomeric compounds to this Drosha recognition region results in a 1.5to 2.5-fold increase in the levels of the pri-miRNA.

As used herein, the term “Drosha cleavage site” is used to refer to asite approximately 22 nucleobases from the junction of the terminalhairpin loop and the stem of a pri-miRNA. One end of the miRNA isdetermined by selection of the cleavage site by the Drosha enzyme.

Identification of miRNAs Deregulated in Leukemic Cell Lines HarboringALL1 Rearrangements.

Applying miRNA microarray analysis, we determined the miRNA expressionprofiles of human leukemic cell lines harboring ALL1 rearrangements. Atotal of 18 miRNAs were found to be upregulated at statisticalsignificance in cell lines with rearranged ALL1, including SEMK2 andRS4;11 cells with the t (4;11) and PER377 cells with the t (9;11). Twopro-B cell lines with no ALL1 abnormalities, 380 and REH, did not showupregulation, as shown in Table 1.

Table 1 shows a comparison of micro RNA expression profiles of cellswith and without ALL1 rearrangement. Micro RNA expression profiles weredetermined in triplicate by probing micro RNA-chip with total RNAs fromthree cell lines expressing ALL-1 fusion protein and two cell linesbearing similar phenotype but lacking ALL-1 abnormalities. Genomic lociof bold typed miRs have been previously identified as binding sites fornormal ALL-1 (14).

TABLE 1 SAM FDR MicroRNA Score* (%)** upregulated micro RNAs hsa-mir-1914.84 0 hsa-mir-24-1 4.42 0 hsa-mir-221 4.27 0 hsa-mir-24-2 3.91 0hsa-mir-192 3.84 0 hsa-mir-222 3.75 0 hsa-mir-196a-1 3.59 0 hsa-mir-023b3.27 0 hsa-mir-146a 3.26 0 hsa-mir-023a 3.10 0 hsa-mir-128b 2.83 0hsa-mir-128a 2.69 0 hsa-mir-220 2.54 0 hsa-mir-196b 2.39 0 hsa-mir-2232.26 0 hsa-mir-146b 2.20 0 hsa-mir-214 1.90 2.46 hsa-mir-135a-1 1.902.46 downregulated micro RNAs hsa-mir-125b-1 −3.86 0 hsa-mir-125b-2−3.19 0 hsa-mir-100 −2.45 2.97 *SAM identifies genes with statisticallysignificant scores (i.e. paired t tests). Each gene is assigned a scoreon the basis of its change in gene expression relative to the standarddeviation of repeated measurements for that gene. Genes with scoresgreater than a threshold are deemed potentially significant. **Thepercentage of such genes identified by chance is the q-value of FalseDiscovery Rate. miR-155 and 27a, investigated in this paper, are notupregulated in the cell lines with ALL1 translocations.

Northern analysis supported and expanded these findings (see FIG. 6). Toconfirm and extend some of the results of the microarrays, theexpression of miR-191, ranked top in the analysis, and miR-155 which didnot show differential expression in lines with ALL1 gene rearrangements,were determined by applying RNase protection assay (see FIG. 1).

While miR-191 mature species could hardly be detected in REH and 380cells, it was abundant in lines expressing All1 fusion proteins,including ML-2 with the t(6;11) chromosome translocation, PER377, SEMK2and RS4;11 cells. In contrast, mature miR-155 was expressed in 380 andREH cells to considerably higher level compared to the other cells. Thisassay also showed that the degree of the pri-miR-191 protection(expression) was similar in all leukemic cells, except for RS4;11,regardless of the expression level of the mature species. This showsthat the higher abundance of mature miR-191 in ALL1 associated leukemiasis not due to overproduction of the pri-miRNA.

All1 Fusion Proteins, All1/Af4 and All1/Af9, Physically Interact withDrosha In Vivo.

The localization of both Drosha and All1 fusion proteins to the cellnuclei indicates that the latter affects Drosha-mediated miR-191processing. To test the physical interaction between Drosha and All1fusion proteins, we applied coimmunoprecipitation methodology. It hasbeen previously reported that the exogenously expressed Drosha:FLAGassembles a complex, termed the microprocessor complex (8, 9, 10). Inaddition, Drosha:FLAG was found to assemble a second and largermultiprotein complex of >2 MDa which contained many RNA binding proteinsincluding EWS (10). We used anti-Drosha Ab to precipitate endogenousDrosha produced in SEMK2 and PER377 cell nuclei.

In parallel, Drosha-Flag was precipitated with anti-Flag mAb from wholecell lysates of transfected K562 cells. Drosha in the immunoprecipitateswere eluted by adding excess amount of the synthetic peptide previouslyused to generate the Ab. The eluates were subjected to Western blotanalysis (see FIG. 2), as well as to in vitro cleavage assays to measureprocessing of miR-191 and miR-155 probes (see FIG. 3).

The Western blot analysis demonstrated co-immunoprecipitation of twoknown Drosha-associated proteins, DGCR8 and EWS (see FIG. 2A).Strikingly, the fusion proteins All1/Af4 and All1/Af9 co-precipitatedwith Drosha (ibid). In contrast, normal p300 All1 did notco-precipitate. Reciprocal immunoprecipitation directed against All1/Af4by using anti-Af4C-terminal Ab failed to co-immunoprecipitate Drosha,although this Ab effectively precipitates the fusion protein (data notshown). The co-immunoprecipitaion of the All1 fusion proteins withDrosha is not due to cross-reaction, because the anti-Drosha Ab did notprecipitate All1/Af4 from SEMK2 cells in which the Drosha protein wasdownregulated by interference RNA (see FIG. 2B).

The failure of anti-Af4 Ab to coprecipitate Drosha indicates that only asmall portion of All1/Af4 is associated with Drosha or that theassociation masks the relevant epitope on Af4 C-terminal region. We nextsought to determine whether the association between All1/Af4 and Droshais RNA-dependent and/or DNA-dependent. To this end, SEMK2 nuclearextracts were treated extensively with either RNase or DNase andsubjected to IP with anti-Drosha Ab. Western blot analysis showed thepresence of All1/Af4, Drosha, DGCR8 and EWS proteins in theimmunoprecipitate of RNase-treated nuclear extracts (FIG. 2B).Significantly, DNase treatment abrogated the association of Drosha withAll1/Af4 while the association with other proteins was sustained (ibid).These results suggest that a genomic DNA is involved in the physicalinteraction between All1/Af4 and the Drosha complex.

The in vitro cleavage assays showed that all Drosha preparationsgenerated three species of miR-191 cleavage products. Of these, thespecies of approx. 66 nucleotides was identified as pre-miR-191 becauseof its cleavage by recombinant Dicer enzyme (see FIG. 3, right).Similarly, the mixture of miR-155 processed products, surmised to becomposed of three species of 55, 59 and 65 nucleotides was shown to befurther cleaved by Dicer, resulting in generation of 22 bases products(ibid). These results indicated that the three affinity-purified Droshapreparations were functionally active with both miR-191 and miR-155templates. Drosha containing All1/Af4 exhibited the strongest processingactivity whereas Drosha containing All1/Af9 had less processingactivity, similar to that of the Drosha:FLAG preparation.

All1/Af4-Mediated Drosha Recruitment to miRNA Loci.

The dependency of the physical interaction between All1/Af4 and Droshaon cellular DNA prompted us to investigate the occupancy of the twoproteins on the miR-191 gene. We have also discovered that normal All1binds to DNA regions located 3.5 and 1.5 kb upstream of miR-191 hairpinas well as to the region spanning the hairpin sequence itself (11).Chromatin immunoprecipitation analysis was done on: 1) SEMK2 cellstransfected with SEMK2-fusion junction-specific siRNA; the latterdownregulates the All1/Af4 protein at an efficiency of >90%, 2) SEMK2cells expressing siRNA which targets a different ALL1/AF4 junction andtherefore does not affect the level of the fusion protein in the cells(the two siRNAs are referred to as SEMJ and MVJ siRNA, respectively; theamount of All1/Af4 protein in the transfectants is shown in FIG. 4A).

The analysis of chromatin of cells containing MVJ siRNA, as well as ofintact SEMK2 cells (not shown), showed co-occupancy of normal All1,All1/Af4 and Drosha proteins on the three regions within the miR-191locus (see FIG. 4B). In contrast, no occupancy of All1/Af4 and Drosha onmiR-155 hairpin was detected (see FIG. 4C).

Knockdown of All1/Af4 by treatment with SEMJ siRNA resulted in reducedoccupancy of the fusion protein on the three sites within the miR-191gene, and a concurrent loss of Drosha binding (see FIG. 4B). Thisindicates All1/Af4-mediated Drosha recruitment onto the miR-191 locus.The investigation was further extended to two additional micro RNA loci.The miR-23a and miR-27a genes are aligned in 5′ to 3′ configuration andare spaced by an interval of 84 nucleotides. The expression microarrayanalysis showed miR-23a, but not miR-27a, to be upregulated in leukemiccells expressing All1 fusion proteins (see Table 1).

The protein binding profiles of normal All1, All1/Af4 and Drosha withinthe miR-23a and 27a regions spanning the hairpin sequences resembled theprofiles of miR-191 and miR-155, respectively (see FIG. 4D).

The binding of both All1/Af4 and Drosha to the miR-23a gene is reducedor eliminated (ibid) in SEMK2 cells knocked out for All1/Af4 (SEMJ).

All1/Af4 knockdown causes accumulation of specific pri-miRNAs.

To investigate the consequence of the reduction in amounts of All1/Af4and Drosha bound to the genomic regions encoding miR-191 and miR-23a, wedetermined the expression level of primary and processed RNA products ofthe loci in comparison to those encoded by the miR-155 and miR-27agenes. The products from SEMK2 cells treated with MVJ siRNA, or SEMJsiRNA or Drosha-specific siRNA were analyzed by RNase protection assay(see FIG. 5).

Both All1/Af4 and Drosha knockdown resulted in accumulation of theprimary transcript of miR-191 and miR-23a indicating impairment ofDrosha function by either manipulation. The apparent impairment causedby both knockdown of Drosha and All1/Af4 is reflected in reducedabundance of the 22 bases mature miR-23a. In contrast, knockdown ofAll1/Af4 in cells treated with SEMJ siRNA did not increase the abundanceof pri-miR-155 or pri-miR-27a compared to cells treated with the inertMVJ siRNA (knockdown of Drosha brought about accumulation of pri-miR-155and pri-miR-27a). This indicates that elimination of All1/Af4 impairsprocessing of pri-miR-191 and pri-miR-23a, but not of pri-miR-155 orpri-miR-27a.

DISCUSSION

Presented herein are several micro RNAs that have been identified asbeing upregulated in ALL1-associated leukemias. Further, we show thatleukemogenic All1 fusion proteins, All1/Af4 and All1/Af9 physicallyinteract with Drosha, the nuclear RNase III enzyme essential for microRNA biogenesis. The notion that nuclear pri-miRNA processing mediated byDrosha and its associated protein(s) greatly affects miRNA production invivo was first noticed in discrepancies between the levels of primarytranscript, precursor, and mature miRNA species. Human embryonic stemcells express measurable amount of the primary transcript encodinglet-7a-1 but lack mature species (12). Similarly, the level of miR-155in diffuse large B cell lymphoma showed only a weak correlation with thelevel of BIC RNA in which miR-155 is contained (13).

Recent study to determine let-7g expression of all three molecular formsin mouse embryo showed that the mature species is detectable at 10.5 dgestation and is high at 14.5, whereas the primary transcript is highlyexpressed throughout development (14). Similar discrepancies were alsofound in several miRNAs known to be associated with mouse development.Since the accumulation of the precursor species was not detected, thedifferentiation events that occur during embryonic development activateDrosha processing of specific miRNA. In the same study, the authorsfurther extended their findings to primary human tumors by comparing thedata sets of primary transcripts and corresponding miRNA expressions andshowed evidence supporting the Drosha processing block, which may causethe down-regulation of miRNAs observed in cancer (ibid). Apparently,exploration of molecular mechanisms underlying activation or inhibitionof Drosha processing, directed against specific miRNA is the next need.

By applying ChIP analysis and RNase protection assay to leukemic cellsexpressing All1/Af4, or impaired in this expression due to enforcedtaking in of siRNA directed against the latter, the inventor herein nowshows recruitment of both All1/Af4 and Drosha to a specific micro RNAgenomic locus, and augmentation of processing of the primary transcript.The apparent enhanced production of the mature micro RNA in cell linesproducing All1 fusion proteins is now believed to be due to Droshabinding to the corresponding locus.

In a particular aspect, there is provided herein a new mechanism bywhich micro RNAs may be regulated, and a new function for All1 leukemicproteins.

Upregulation of miR-191 is found to be associated with poor prognosis inacute myeloid leukemias (15). Upregulation of miR-191 is also observedin study of 6 different types of solid tumors including colon, breastand lung cancer (16)

EXAMPLES Materials and Methods

Cell Culture and Antibodies.

Human pro-B ALL 380, pre-B ALL 697, ML-2 with the t(6;11), and SEMK2 andMV4;11 with the t(4;11) were obtained from DSMZ. REH pro-B ALL, RS4;11with the t(4;11) and K562 were purchased from ATCC. PER377 with thet(9;11) was obtained from Dr. Ursulla Kees. All cell lines weremaintained in RPMI 1640 medium supplemented with 10% fetal bovine serum.Antibodies against Drosha (ab12286), DGCR8 (ab24162) and a Droshasynthetic peptide (ab12307) were purchased from Abcam. Ab against EWSwas made by Bethyl Laboratories (A300-308A). Anti-FLAG M2 mAb and 3×FLAGpeptide were obtained from Sigma. Ab 169 directed against ALL-1N-terminus was described (17). Ab against AF4 C-terminus was generatedin rabbit by using bacterially synthesized polypeptide spanning AF4residues 2323-2886.

Microarray Analysis.

Microarray analysis was performed as previously described (18). Raw datawere normalized and analyzed in GENESPRING 7.2 software (zcomSiliconGenetics, Redwood City, Calif.). Expression data were median-centered byusing both the GENESPRING normalization option and the global mediannormalization of the BIOCONDUCTOR package (www.bioconductor.org) withsimilar results. Statistical comparisons were done by using theGENESPRING ANOVA tool and the significance analysis of microarray (SAM)software.

miRNA Detection.

RNase Protection assays (RPA) were performed using RPA III kit fromAmbion, according to the manufacturer's instructions. 5-20 μg of totalRNA extracted with TRIZOL reagent (Invitrogen) were used per reaction.Cyclophillin antisense control template was obtained from Ambion and waslabeled by utilizing T7 RNA polymerase. For the identification ofprotected species corresponding to pri-, pre- and mature miR-191 andmiR-155, see FIG. 7.

Vector Construction and Probe Preparation.

A genomic fragment spanning miR-191 hairpin was prepared by digestingBAC clone RP13-131K19 with PflMI-Bsu36I, blunt-ending and subcloninginto the SmaI site of pGEM-3Z (Promega) in both orientations. Theseconstructs were linearlized with BamHI and used as templates forgenerating RNA probes by using Riboprobe in vitro transcription kit withT7 RNA polymerase (Promega). Probes with sense and anti-senseorientation were purified on a denaturing gel, and used in in vitrocleavage assay and in RNase protection assay, respectively. miR-155hairpin region, embedded within the third exon of the BIC gene, wasPCR-amplified from the human IMAGE cDNA clone 5176657.

The forward primer ATGCCTCATCCTCTGAGTGCT [SEQ ID NO: 1] tethered withEcoRI site and the reverse primer CTCCCACGGCAGCAATTTGTT [SEQ ID NO: 2]tethered with HindIII site, corresponding to nucleotides 261-281 and401-421 (ref. 13), respectively, were used for amplification.

Subsequently, the PCR product was cloned into the EcoRI-HindIII sites ofthe pGEM-3Z vector. Sense and anti-sense RNA probes were synthesized byusing T7 RNA polymerase and SP6 RNA polymerase, respectively. Genomicregions spanning miR-23a and miR-27a hairpin sequences werePCR-amplified as shown in FIG. 8 and cloned into the HindIII-EcoRI sitesof the pGEM3Z vector.

Anti-*SAM identifies genes with statistically significant scores (i.e.paired t tests). Each gene is assigned a score on the basis of itschange in gene expression relative to the standard deviation of repeatedmeasurements for that gene. Genes with scores greater than a thresholdare deemed potentially significant.

**The percentage of such genes identified by chance is the q-value ofFalse Discovery Rate. miR-155 and 27a, investigated in this paper, arenot upregulated in the cell lines with ALL1 translocations.

Probes of miR-23a and miR-27a were prepared by digesting therecombinants with NaeI and Bsu36I, respectively, followed by in vitrotranscription with Sp6 RNA polymerase.

Immunoprecipitation.

K562 cells were transfected with pCK-drosha-flag by using a Nucleofectorapparatus according to the manufacturer's instructions (AMAXA). 2×10⁸transfected cells were lysed and subjected to IP with anti-Flag M2 mAbas described in ref. 11. Briefly, 25 mg whole cell lysate were incubatedwith 500 μg mAb after preclearing with protein G Sepharose (GEHealthcare) at 4° C., 0/N. Immunocomplex was precipitated with protein GSepharose, washed, and the Drosha:FLAG in the precipitate was eluted byadding 3×FLAG peptide at a concentration of 0.4 mg/ml in a buffercontaining 30 mM Hepes, pH7.4/100 mM KCl/5% Glycerol/0.2 mM EDTA/7.5 mMMgCl₂/2 mM DTT. Elution was repeated three times, each for 30 min at RT,and eluates were combined. For immunoprecipitation of endogenous Drosha,50 mg of nuclear extracts from SEMK2 or PER377 cells prepared by themethod of Dignam et al. (19) were subjected to IP with 300 μg ofanti-Drosha Ab. The anti-Drosha Ab, purchased from Abcam, was generatedin rabbit by immunizing with a synthetic peptide derived from theN-terminal region of Drosha, and the peptide is commercially available.

The examples with small scale IP showed that the addition of excessDrosha peptide to anti-Drosha-immunoprecipitate releases Drosha; thisprocedure enabled purification of the Drosha complex in a native form.The peptide was used for the elution of Drosha at a concentration of 0.4mg/ml. In some IPs, as shown in FIG. 2B, 250 μg of SEMK2 nuclear extactswere mixed either with 50 μL of DNase-free RNase (Roche) or with 50 U ofRQ1 DNase (Promega) and subjected to preclearing with protein ASepharose (GE Healthcare) at RT for 60 min. This was followed by IP with10 μg of anti-Drosha Ab.

In Vitro Processing of Pri-miRNAs.

In vitro processing assay was done essentially as described (8). Amountsto be added of Drosha:FLAG and of two Drosha preparations weredetermined by measuring the content of Drosha by Western blot analysis.Briefly, 20 μL of reaction mixtures containing immuno-purified Drosha,7.5 mM MgCl₂, 20 U of RNase inhibitor (RNasin, Promega), 2 mM ATP, 2 mMDTT and 1×10⁵ cpm of the labeled probe were incubated at 37° C. for 90min. The reactions were terminated by adding 20 μL of buffer containing20 mM Tris, pH8.0/10 mM EDTA/1% SDS/2 μg of proteinase K (Roche),followed by incubation at 45° C. for 30 min. After extraction withphenol/chloroform and chloroform, the processed products wereethanol-precipitated and resolved on a polyacrylamide gel containing 8Murea.

RNA Interference

siRNA duplexes targeting ALL-1/AF4 and Drosha mRNAs in SEMK2 cells weretransfected by applying the Amaxa Nucleofector using kit V and programT-20. 24 h after transfection, cells were harvested and subjected to asecond transfection, and subsequently were grown in culture foradditional 48 h. Target sequences of SEMJ siRNA and MVJ siRNA were5′-AAGAAAAGCAGACCUACUCCA-3′ [SEQ ID NO: 3], and5′-AAGAAAAGGAAAUGACCCATT-3′ [SEQ ID NO: 4], respectively.

The former si RNA targets ALL-1/AF4 mRNA produced in SEMK2 cells, whilethe latter targets ALL-1/AF4 mRNA produced in MV4;11 cells. Note thatthe first 8 nucleotides in both siRNAs correspond to ALL-1 mRNA sequenceimmediately 5′ of the fusion point and are identical whereas thefollowing 13 nucleotides correspond to AF4 sequences which vary betweenthe fusions and accordingly between the siRNAs; thus, MVJ siRNA will beinactive in SEMK2 cells. The sequence of Drosha siRNA is from ref. 10.The siRNAs were synthesized by Dharmacon.

Chromatin Immunoprecipitation (ChIP) Assay.

ChIP assays were performed using the ChIP assay kit from Upstate withminor modifications. Briefly, 5×10⁷ formaldehyde-treated SEMK2 cellswere lysed in 1 mL buffer containing 50 mM Hepes, pH7.4/140 mM NaCl/1%Triton X/0.1% Na-Deoxycholate/1× Complete protease inhibitor (Roche). 50μL aliquot of the preparation was treated to reverse the cross-linking,deproteinized with proteinase K, extracted with phenol chloroform anddetermined for DNA concentration. An aliquot of chromatin preparationcontaining 25 μg DNA was used per ChIP. DNase free RNase (Roche) wasadded at a concentration of 200 μg/mL during reverse cross linking Afterdeproteiniztion with proteinase K, DNA was purified in 50 μL TE by usingPCR-purification kit (QIAGEN) according to the manufacturer'sinstructions. 1 μL aliquot was used for PCR. Primer sequences are listedin Table 2.

TABLE 2 Sequences of primers used in ChIP analysis in FIG. 4 (shown 5′to 3′) ChIP analyzed region Forward primer Reverse primer3.5 kb upstream of GTAGCTGCCACTACCACAGAT AGCCAGAGTCAGATGCTCAGTmiR-191 hairpin [SEQ ID NO: 5] [SEQ ID NO: 6] 1.5 kb upstream ofTACAAGCTACGTAGCGCGAGA ACTCGGCCTCCTAAGACTGAGG miR-191 hairpin[SEQ ID NO: 7] [SEQ ID NO: 8] miR-191 hairpin GTTCCCTCTAGACTCAGTCACTACCATTGC AGCCCTA CGTTTCA [SEQ ID NO: 10] [SEQ ID NO: 9]miR-155 hairpin TGAGCTCCTTCCTTTCAACAG GTTGAACATCCCAGTGACCAG[SEQ ID NO: 11] [SEQ ID NO: 12] miR-23a hairpin TCTAGGTATCTCTGCCTCTCCAAGCATCCTCGGTGGCAGAGCTCA [SEQ ID NO: 13] [SEQ ID NO: 14] miR-27a hairpinTGAGCTCTGCCACCGAGGATGCT ACAGGCGGCAAGGCCAGAGGA [SEQ ID NO: 15][SEQ ID NO: 16]

Diagnostics, Drug Discovery and Therapeutics

The oligomeric compounds and compositions of the present invention canadditionally be utilized for research, drug discovery, kits anddiagnostics, and therapeutics.

For use in research, oligomeric compounds of the present invention areused to interfere with the normal function of the nucleic acid moleculesto which they are targeted. Expression patterns within cells or tissuestreated with one or more oligomeric compounds or compositions of theinvention are compared to control cells or tissues not treated with thecompounds or compositions and the patterns produced are analyzed fordifferential levels of nucleic acid expression as they pertain, forexample, to disease association, signaling pathway, cellularlocalization, expression level, size, structure or function of the genesexamined. These analyses can be performed on stimulated or unstimulatedcells and in the presence or absence of other compounds that affectexpression patterns.

For use in drug discovery, oligomeric compounds of the present inventionare used to elucidate relationships that exist between small non-codingRNAs, genes or proteins and a disease state, phenotype, or condition.These methods include detecting or modulating a target comprisingcontacting a sample, tissue, cell, or organism with the oligomericcompounds and compositions of the present invention, measuring thelevels of the target and/or the levels of downstream gene productsincluding mRNA or proteins encoded thereby, a related phenotypic orchemical endpoint at some time after treatment, and optionally comparingthe measured value to an untreated sample, a positive control or anegative control. These methods can also be performed in parallel or incombination with other experiments to determine the function of unknowngenes for the process of target validation or to determine the validityof a particular gene product as a target for treatment or prevention ofa disease.

For use in kits and diagnostics, the oligomeric compounds andcompositions of the present invention, either alone or in combinationwith other compounds or therapeutics, can be used as tools indifferential and/or combinatorial analyses to elucidate expressionpatterns of a portion or the entire complement of non-coding or codingnucleic acids expressed within cells and tissues.

The specificity and sensitivity of compounds and compositions can alsobe harnessed by those of skill in the art for therapeutic uses.Antisense oligomeric compounds have been employed as therapeuticmoieties in the treatment of disease states in animals, includinghumans. Antisense oligonucleotide drugs, including ribozymes, have beensafely and effectively administered to humans and numerous clinicaltrials are presently underway. It is thus established that oligomericcompounds can be useful therapeutic modalities that can be configured tobe useful in treatment regimes for the treatment of cells, tissues andanimals, especially humans.

For therapeutics, an animal, preferably a human, suspected of having adisease or disorder presenting conditions that can be treated,ameliorated, or improved by modulating the expression of a selectedsmall non-coding target nucleic acid is treated by administering thecompounds and compositions. For example, in one non-limiting embodiment,the methods comprise the step of administering to or contacting theanimal, an effective amount of a modulator or mimic to treat, ameliorateor improve the conditions associated with the disease or disorder. Thecompounds effectively modulate the activity or function of the smallnon-coding RNA target or inhibit the expression or levels of the smallnon-coding RNA target. In certain embodiments, the small non-coding RNAtarget is a polycistronic pri-miRNA, a monocistronic pri-miRNA, apre-miRNA, or a miRNA. In additional embodiments, the small non-codingRNA target is a single member of a miRNA family. Alternatively, two ormore members of an miRNA family are selected for modulation. In afurther embodiment, the small non-coding RNA target is a selectivelyprocessed miRNA. In one embodiment, the level, activity or expression ofthe target in an animal is inhibited by about 10%. In another embodimentthe level, activity or expression of a target in an animal is inhibitedby about 30%. Further, the level, activity or expression of a target inan animal is inhibited by 50% or more, by 60% or more, by 70% or more,by 80% or more, by 90% or more, or by 95% or more.

In another embodiment, the present invention provides for the use of acompound of the invention in the manufacture of a medicament for thetreatment of any and all conditions associated with miRNAs and miRNAfamilies.

The reduction of target levels may be measured in serum, adipose tissue,liver or any other body fluid, tissue or organ of the animal known tocontain the small non-coding RNA or its precursor. Further, the cellscontained within the fluids, tissues or organs being analyzed contain anucleic acid molecule of a downstream target regulated or modulated bythe small non-coding RNA target itself.

Compositions and Methods for Formulating Pharmaceutical Compositions

In another aspect, there is provided herein pharmaceutical compositionsand formulations that include the oligomeric compounds, small non-codingRNAs and compositions of the invention. Compositions and methods for theformulation of pharmaceutical compositions are dependent upon a numberof criteria, including, but not limited to, route of administration,extent of disease, or dose to be administered. Such considerations arewell understood by those skilled in the art.

The oligomeric compounds and compositions of the invention can beutilized in pharmaceutical compositions by adding an effective amount ofthe compound or composition to a suitable pharmaceutically acceptablediluent or carrier. Use of the oligomeric compounds and methods of theinvention may also be useful prophylactically.

The oligomeric compounds and compositions encompass any pharmaceuticallyacceptable salts, esters, or salts of such esters, or any other compoundwhich, upon administration to an animal, including a human, is capableof providing (directly or indirectly) the biologically active metaboliteor residue thereof. Accordingly, for example, the disclosure is alsodrawn to prodrugs and pharmaceutically acceptable salts of theoligomeric compounds of the invention, pharmaceutically acceptable saltsof such prodrugs, and other bioequivalents.

The term “prodrug” indicates a therapeutic agent that is prepared in aninactive form that is converted to an active form (i.e., drug) withinthe body or cells thereof by the action of endogenous enzymes or otherchemicals and/or conditions.

The term “pharmaceutically acceptable salts” refers to physiologicallyand pharmaceutically acceptable salts of the compounds and compositionsof the invention: i.e., salts that retain the desired biologicalactivity of the parent compound and do not impart undesiredtoxicological effects thereto. Suitable examples include, but are notlimited to, sodium and potassium salts.

In some embodiments, an oligomeric compound can be administered to asubject via an oral route of administration. The subject may be amammal, such as a mouse, a rat, a dog, a guinea pig, or a non-humanprimate. In some embodiments, the subject may be a human or a humanpatient. In certain embodiments, the subject may be in need ofmodulation of the level or expression of one or more pri-miRNAs asdiscussed in more detail herein. In some embodiments, compositions foradministration to a subject will comprise modified oligonucleotideshaving one or more modifications, as described herein.

Cell Culture and Oligonucleotide Treatment

The effects of oligomeric compounds on target nucleic acid expression orfunction can be tested in any of a variety of cell types provided thatthe target nucleic acid is present at measurable levels. This can bereadily determined by methods routine in the art, for example Northernblot analysis, ribonuclease protection assays, or real-time PCR. Celltypes used for such analyses are available from commercial vendors (e.g.American Type Culture Collection, Manassus, Va.; Zen-Bio, Inc., ResearchTriangle Park, N.C.; Clonetics Corporation, Walkersville, Md.) and cellsare cultured according to the vendor's instructions using commerciallyavailable reagents (e.g. Invitrogen Life Technologies, Carlsbad, Calif.

Any of the methods for gene therapy available in the art can be usedaccording to the present invention. For general reviews of the methodsof gene therapy, see Goldspiel et al., 1993, Clinical Pharmacy 12:488505; Wu and Wu, 1991, Biotherapy 3:87 95; Tolstoshev, 1993, Ann. Rev.Pharmacol. Toxicol. 32:573 596; Mulligan, 1993, Science 260:926 932; andMorgan and Anderson, 1993, Ann. Rev. Biochem. 62:191 217; May, 1993,TIBTECH 11(5):155 215). Methods commonly known in the art of recombinantDNA technology which can be used are described in Ausubel et al. (eds.),1993, Current Protocols in Molecular Biology, John Wiley & Sons, NY; andKriegler, 1990, Gene Transfer and Expression, A Laboratory Manual,Stockton Press, NY.

While the invention has been described with reference to various andpreferred embodiments, it should be understood by those skilled in theart that various changes may be made and equivalents may be substitutedfor elements thereof without departing from the essential scope of theinvention. In addition, many modifications may be made to adapt aparticular situation or material to the teachings of the inventionwithout departing from the essential scope thereof. Therefore, it isintended that the invention not be limited to the particular embodimentdisclosed herein contemplated for carrying out this invention, but thatthe invention will include all embodiments falling within the scope ofthe claims.

REFERENCES

The relevant teachings of all publications cited herein that have notexplicitly been incorporated by reference, are incorporated herein byreference in their entirety. While this invention has been particularlyshown and described with references to preferred embodiments thereof, itwill be understood by those skilled in the art that various changes inform and details may be made therein without departing from the scope ofthe invention encompassed by the appended claims. Citation of areference herein shall not be construed as an admission that suchreference is prior art to the present invention.

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What is claimed is:
 1. A method of diagnosing whether a subject has, oris at risk for developing, acute lymphomic leukemia (ALL), comprising:measuring the level of at least miR-146a gene product in a test samplefrom the subject, wherein an increase in the level of the miR geneproduct in the test sample, relative to the level of a corresponding miRgene product in a control sample, is indicative of the subject eitherhaving, or being at risk for developing, ALL.
 2. A method of determiningthe prognosis of a subject with ALL cancer, comprising: measuring thelevel of at least miR-222 gene product in a test sample from thesubject, wherein the miR gene product is associated with an adverseprognosis in ALL; and wherein an increase in the level of the at leastone miR gene product in the test sample, relative to the level of acorresponding miR gene product in a control sample, is indicative of anadverse prognosis.
 3. A method of diagnosing whether a subject has, oris at risk for developing, ALL, comprising: (1) reverse transcribing RNAfrom a test sample obtained from the subject to provide a set of targetoligodeoxynucleotides; (2) hybridizing the target oligodeoxynucleotidesto a microarray comprising at least one miR-222 miRNA-specific probeoligonucleotide to provide a hybridization profile for the test sample;and (3) comparing the test sample hybridization profile to ahybridization profile generated from a control sample, wherein anupregulated signal of at least one miRNA, relative to the signalgenerated from the control sample, is indicative of the subject eitherhaving, or being at risk for developing, ALL.
 4. A method of diagnosingwhether a subject has, or is at risk for developing, ALL with an adverseprognosis in a subject, comprising: (1) reverse transcribing RNA from atest sample obtained from the subject to provide a set of targetoligodeoxynucleotides; (2) hybridizing the target oligodeoxynucleotidesto a microarray comprising at least one miR-222 miRNA-specific probeoligonucleotide to provide a hybridization profile for the test sample;and (3) comparing the test sample hybridization profile to ahybridization profile generated from a control sample, wherein anupregulated signal of at least one miRNA, relative to the signalgenerated from the control sample, is indicative of the subject eitherhaving, or being at risk for developing, ALL.